Starting phenix.real_space_refine on Sun Sep 13 06:16:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tib_25616/09_2026/7tib_25616.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tib_25616/09_2026/7tib_25616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tib_25616/09_2026/7tib_25616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tib_25616/09_2026/7tib_25616.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tib_25616/09_2026/7tib_25616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tib_25616/09_2026/7tib_25616.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tib_25616/09_2026/7tib_25616.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tib_25616/09_2026/7tib_25616.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 55 5.49 5 Mg 4 5.21 5 S 101 5.16 5 C 13381 2.51 5 N 3631 2.21 5 O 4205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 174 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21377 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3923 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 19, 'TRANS': 475} Chain: "B" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2505 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2586 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "D" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2687 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 327} Chain: "E" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2716 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain breaks: 1 Chain: "F" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2003 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "G" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1983 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain breaks: 1 Chain: "H" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1964 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 8, 'TRANS': 241} Chain breaks: 3 Chain: "I" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 488 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "J" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.30, per 1000 atoms: 0.20 Number of scatterers: 21377 At special positions: 0 Unit cell: (127.2, 133.56, 125.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 101 16.00 P 55 15.00 Mg 4 11.99 O 4205 8.00 N 3631 7.00 C 13381 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 645.5 milliseconds 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4910 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 16 sheets defined 52.9% alpha, 15.0% beta 8 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.537A pdb=" N VAL A 310 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.708A pdb=" N ASN A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 392 through 396 removed outlier: 3.726A pdb=" N LEU A 396 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 407 removed outlier: 4.153A pdb=" N PHE A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 417 removed outlier: 3.974A pdb=" N LYS A 417 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 429 Processing helix chain 'A' and resid 435 through 444 removed outlier: 3.861A pdb=" N GLN A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 479 through 494 removed outlier: 3.822A pdb=" N ILE A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 513 through 525 Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 565 through 570 removed outlier: 4.176A pdb=" N ARG A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 4.146A pdb=" N ASP A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 595 Processing helix chain 'A' and resid 609 through 632 Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 668 through 695 removed outlier: 5.442A pdb=" N LEU A 692 " --> pdb=" O TYR A 688 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLY A 693 " --> pdb=" O HIS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 705 removed outlier: 3.597A pdb=" N ASP A 704 " --> pdb=" O GLY A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 714 removed outlier: 4.104A pdb=" N LYS A 711 " --> pdb=" O PRO A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 721 removed outlier: 3.785A pdb=" N LEU A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 721 " --> pdb=" O PHE A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.630A pdb=" N TYR A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 746 removed outlier: 3.709A pdb=" N MET A 746 " --> pdb=" O TRP A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 762 Processing helix chain 'A' and resid 763 through 775 removed outlier: 3.587A pdb=" N ASN A 775 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.604A pdb=" N ILE B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 4.079A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.767A pdb=" N ARG B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.775A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.605A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 255 Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 281 through 300 removed outlier: 3.624A pdb=" N ARG B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 320 removed outlier: 3.676A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 322 No H-bonds generated for 'chain 'B' and resid 321 through 322' Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.571A pdb=" N ASN C 12 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.766A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 removed outlier: 3.508A pdb=" N THR C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 103 removed outlier: 4.016A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.534A pdb=" N ALA C 121 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 removed outlier: 4.410A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 190 through 200 Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 253 Processing helix chain 'C' and resid 255 through 270 removed outlier: 3.732A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 293 through 311 Processing helix chain 'C' and resid 315 through 332 Processing helix chain 'D' and resid 15 through 24 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.737A pdb=" N VAL D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 88 Proline residue: D 85 - end of helix Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.870A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.695A pdb=" N LEU D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN D 128 " --> pdb=" O HIS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 removed outlier: 3.562A pdb=" N SER D 144 " --> pdb=" O GLU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 160 removed outlier: 3.571A pdb=" N LEU D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 193 through 208 removed outlier: 5.155A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 225 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.700A pdb=" N LEU D 245 " --> pdb=" O GLY D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 removed outlier: 3.958A pdb=" N LEU D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 296 through 311 Processing helix chain 'D' and resid 315 through 334 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.595A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.447A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.531A pdb=" N VAL E 65 " --> pdb=" O GLY E 62 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR E 66 " --> pdb=" O PRO E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 66' Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.564A pdb=" N ASP E 100 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 102 through 103 No H-bonds generated for 'chain 'E' and resid 102 through 103' Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.748A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 4.045A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR E 161 " --> pdb=" O THR E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.846A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 291 removed outlier: 3.539A pdb=" N GLU E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 337 through 353 removed outlier: 3.726A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY E 344 " --> pdb=" O PHE E 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 18 removed outlier: 3.616A pdb=" N LYS F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 81 removed outlier: 3.575A pdb=" N CYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 152 Processing helix chain 'F' and resid 209 through 216 removed outlier: 3.830A pdb=" N ASP F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 221 removed outlier: 3.718A pdb=" N SER F 220 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 19 removed outlier: 4.470A pdb=" N PHE G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.662A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 removed outlier: 3.682A pdb=" N SER G 194 " --> pdb=" O PRO G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 217 removed outlier: 3.927A pdb=" N LEU G 212 " --> pdb=" O GLY G 208 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 19 removed outlier: 4.452A pdb=" N PHE H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE H 19 " --> pdb=" O ILE H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 82 removed outlier: 3.782A pdb=" N GLY H 82 " --> pdb=" O ILE H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 209 through 216 removed outlier: 3.699A pdb=" N ASP H 214 " --> pdb=" O LYS H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 221 removed outlier: 4.404A pdb=" N SER H 220 " --> pdb=" O LYS H 217 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU H 221 " --> pdb=" O GLY H 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 217 through 221' Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 377 removed outlier: 8.003A pdb=" N ILE A 452 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE A 421 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE A 454 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET A 423 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 498 removed outlier: 7.746A pdb=" N LYS A 497 " --> pdb=" O ILE A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 601 Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.305A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.570A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.213A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.568A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 213 removed outlier: 5.992A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 57 through 62 removed outlier: 4.940A pdb=" N LEU F 88 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP H 172 " --> pdb=" O SER H 157 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER H 157 " --> pdb=" O ASP H 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 5.649A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 203 through 208 removed outlier: 5.543A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU G 88 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU G 3 " --> pdb=" O TYR G 60 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR G 60 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS G 5 " --> pdb=" O GLN G 58 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.362A pdb=" N LEU G 25 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL G 40 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER G 230 " --> pdb=" O PRO G 234 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 178 through 182 Processing sheet with id=AB5, first strand: chain 'H' and resid 57 through 62 removed outlier: 6.415A pdb=" N LYS H 5 " --> pdb=" O GLN H 58 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR H 60 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU H 3 " --> pdb=" O TYR H 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 47 through 53 removed outlier: 3.796A pdb=" N ASN H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N VAL H 40 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU H 25 " --> pdb=" O VAL H 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 196 through 199 1085 hydrogen bonds defined for protein. 3081 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7004 1.36 - 1.51: 5611 1.51 - 1.66: 9032 1.66 - 1.80: 96 1.80 - 1.95: 63 Bond restraints: 21806 Sorted by residual: bond pdb=" C3' DT J 19 " pdb=" C2' DT J 19 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DT I 15 " pdb=" C2' DT I 15 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.76e+00 bond pdb=" C3' DA I 16 " pdb=" C2' DA I 16 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.76e+00 bond pdb=" C3' DT I 7 " pdb=" C2' DT I 7 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.27e+00 bond pdb=" C3' DT I 9 " pdb=" C2' DT I 9 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 5.96e+00 ... (remaining 21801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 29093 1.70 - 3.40: 508 3.40 - 5.10: 45 5.10 - 6.80: 12 6.80 - 8.50: 1 Bond angle restraints: 29659 Sorted by residual: angle pdb=" O4' DA J 5 " pdb=" C4' DA J 5 " pdb=" C3' DA J 5 " ideal model delta sigma weight residual 106.00 103.38 2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J 15 " pdb=" C4 DT J 15 " pdb=" O4 DT J 15 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT I 10 " pdb=" C4 DT I 10 " pdb=" O4 DT I 10 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT I 26 " pdb=" C4 DT I 26 " pdb=" O4 DT I 26 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 29654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.56: 12348 26.56 - 53.12: 785 53.12 - 79.68: 98 79.68 - 106.25: 18 106.25 - 132.81: 4 Dihedral angle restraints: 13253 sinusoidal: 5711 harmonic: 7542 Sorted by residual: dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 72.81 -132.81 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 46.54 -106.54 1 2.00e+01 2.50e-03 3.08e+01 dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 29.75 -89.75 1 2.00e+01 2.50e-03 2.39e+01 ... (remaining 13250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2060 0.028 - 0.056: 904 0.056 - 0.085: 303 0.085 - 0.113: 157 0.113 - 0.141: 27 Chirality restraints: 3451 Sorted by residual: chirality pdb=" CA VAL E 122 " pdb=" N VAL E 122 " pdb=" C VAL E 122 " pdb=" CB VAL E 122 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA GLU F 129 " pdb=" N GLU F 129 " pdb=" C GLU F 129 " pdb=" CB GLU F 129 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE G 111 " pdb=" N ILE G 111 " pdb=" C ILE G 111 " pdb=" CB ILE G 111 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 3448 not shown) Planarity restraints: 3618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 221 " -0.034 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO C 222 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 222 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 222 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 10 " 0.019 2.00e-02 2.50e+03 1.02e-02 2.61e+00 pdb=" N1 DT I 10 " -0.025 2.00e-02 2.50e+03 pdb=" C2 DT I 10 " -0.000 2.00e-02 2.50e+03 pdb=" O2 DT I 10 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DT I 10 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 10 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 10 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DT I 10 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 10 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT I 10 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 201 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO H 202 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO H 202 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 202 " 0.020 5.00e-02 4.00e+02 ... (remaining 3615 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 303 2.66 - 3.22: 19599 3.22 - 3.78: 33296 3.78 - 4.34: 46224 4.34 - 4.90: 75141 Nonbonded interactions: 174563 Sorted by model distance: nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 2.099 2.170 nonbonded pdb=" O3G AGS B 401 " pdb="MG MG B 402 " model vdw 2.104 2.170 nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 402 " model vdw 2.106 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.146 2.170 nonbonded pdb=" O3G AGS C 401 " pdb="MG MG C 402 " model vdw 2.150 2.170 ... (remaining 174558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 1 through 82 or resid 85 through 104 or resid 106 through \ 173 or resid 177 through 240 or resid 244 through 255)) selection = (chain 'G' and (resid 1 through 82 or resid 85 through 104 or resid 106 through \ 240 or resid 244 through 255)) selection = (chain 'H' and (resid 1 through 173 or resid 177 through 255)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.160 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21806 Z= 0.182 Angle : 0.551 8.499 29659 Z= 0.367 Chirality : 0.039 0.141 3451 Planarity : 0.003 0.052 3618 Dihedral : 16.737 132.807 8343 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.09 % Allowed : 9.02 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.15), residues: 2555 helix: -0.62 (0.14), residues: 1202 sheet: -1.27 (0.20), residues: 525 loop : -2.12 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 224 TYR 0.007 0.001 TYR F 211 PHE 0.017 0.001 PHE G 185 TRP 0.004 0.001 TRP A 669 HIS 0.003 0.000 HIS G 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.18 (21806) covalent geometry : angle 0.55118 / 0.37 (29659) hydrogen bonds : bond 0.14005 / 9.41 ( 1105) hydrogen bonds : angle 5.54526 / 3.98 ( 3121) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 644 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.7833 (mttt) cc_final: 0.7266 (mtmt) REVERT: A 388 LEU cc_start: 0.8396 (mt) cc_final: 0.8159 (mt) REVERT: A 594 GLU cc_start: 0.8111 (tp30) cc_final: 0.7852 (tp30) REVERT: A 604 LEU cc_start: 0.8376 (mt) cc_final: 0.8078 (mt) REVERT: A 630 LYS cc_start: 0.8191 (mttt) cc_final: 0.7978 (mttm) REVERT: A 691 ARG cc_start: 0.7755 (tpt170) cc_final: 0.7552 (tpt-90) REVERT: B 77 GLU cc_start: 0.6885 (tt0) cc_final: 0.6668 (tt0) REVERT: B 202 MET cc_start: 0.8970 (tpp) cc_final: 0.8640 (tpp) REVERT: B 237 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8405 (ttmm) REVERT: C 19 TYR cc_start: 0.8862 (m-80) cc_final: 0.8511 (m-80) REVERT: C 249 LYS cc_start: 0.8507 (tttt) cc_final: 0.8277 (ttmm) REVERT: C 333 ASN cc_start: 0.8024 (t0) cc_final: 0.7791 (t0) REVERT: D 80 LYS cc_start: 0.8349 (mttt) cc_final: 0.8121 (ttpp) REVERT: D 115 ARG cc_start: 0.7963 (ttp-110) cc_final: 0.7017 (mtm-85) REVERT: D 204 ILE cc_start: 0.9408 (mm) cc_final: 0.9076 (mt) REVERT: D 208 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8558 (mm-30) REVERT: E 24 ASN cc_start: 0.7470 (m-40) cc_final: 0.7224 (m-40) REVERT: E 160 LYS cc_start: 0.8275 (tptt) cc_final: 0.7990 (ttpt) REVERT: E 265 LYS cc_start: 0.8556 (mtmt) cc_final: 0.8193 (mttm) REVERT: F 42 ASP cc_start: 0.7119 (t0) cc_final: 0.6848 (t0) REVERT: F 188 MET cc_start: 0.7329 (mmt) cc_final: 0.6322 (mpp) REVERT: G 38 GLN cc_start: 0.8112 (pt0) cc_final: 0.7850 (pt0) REVERT: G 64 HIS cc_start: 0.6877 (p-80) cc_final: 0.6632 (p-80) REVERT: G 124 ASP cc_start: 0.5915 (p0) cc_final: 0.5449 (p0) REVERT: G 247 GLN cc_start: 0.7831 (mt0) cc_final: 0.7503 (mt0) REVERT: H 72 LEU cc_start: 0.5728 (mm) cc_final: 0.5392 (mm) REVERT: H 116 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5770 (tp) REVERT: H 131 LEU cc_start: 0.6085 (mt) cc_final: 0.5779 (mp) outliers start: 25 outliers final: 17 residues processed: 664 average time/residue: 0.1658 time to fit residues: 162.9379 Evaluate side-chains 530 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 512 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.0170 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 GLN A 322 ASN A 364 HIS A 413 ASN A 501 ASN A 537 ASN A 672 GLN A 775 ASN B 18 GLN B 92 GLN B 279 GLN B 317 HIS B 320 ASN C 221 ASN C 292 ASN C 317 GLN C 333 ASN D 128 ASN D 236 GLN D 303 GLN E 18 HIS E 19 ASN E 86 ASN E 103 ASN E 133 HIS F 27 ASN F 38 GLN F 58 GLN G 94 ASN H 27 ASN H 153 GLN H 247 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.171917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.125496 restraints weight = 24517.538| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.84 r_work: 0.3046 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 21806 Z= 0.219 Angle : 0.627 9.112 29659 Z= 0.323 Chirality : 0.044 0.163 3451 Planarity : 0.005 0.063 3618 Dihedral : 14.752 124.527 3283 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.14 % Allowed : 15.34 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.16), residues: 2555 helix: 0.33 (0.15), residues: 1199 sheet: -0.90 (0.21), residues: 521 loop : -1.58 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 267 TYR 0.015 0.002 TYR B 15 PHE 0.014 0.002 PHE B 142 TRP 0.012 0.001 TRP A 638 HIS 0.006 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (21806) covalent geometry : angle 0.62724 / 0.32 (29659) hydrogen bonds : bond 0.04306 / 2.84 ( 1105) hydrogen bonds : angle 4.53918 / 3.21 ( 3121) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 530 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.7961 (mttt) cc_final: 0.7324 (mtmt) REVERT: A 318 MET cc_start: 0.7725 (mmm) cc_final: 0.7319 (mmm) REVERT: A 350 MET cc_start: 0.7650 (tpp) cc_final: 0.7277 (tpp) REVERT: A 474 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: A 594 GLU cc_start: 0.8813 (tp30) cc_final: 0.8447 (tp30) REVERT: A 600 ARG cc_start: 0.7405 (ptp-110) cc_final: 0.7148 (ptp-110) REVERT: A 604 LEU cc_start: 0.8609 (mt) cc_final: 0.8305 (mt) REVERT: A 767 LYS cc_start: 0.6157 (mtmm) cc_final: 0.5948 (mtmm) REVERT: B 115 GLU cc_start: 0.9219 (mp0) cc_final: 0.8237 (mp0) REVERT: B 146 GLN cc_start: 0.8432 (mt0) cc_final: 0.8224 (mm-40) REVERT: B 165 LYS cc_start: 0.8680 (mttp) cc_final: 0.8349 (mttm) REVERT: B 237 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8678 (ttmm) REVERT: C 78 MET cc_start: 0.8706 (mpp) cc_final: 0.8397 (mpp) REVERT: C 207 ARG cc_start: 0.8668 (tpt-90) cc_final: 0.8249 (tpt90) REVERT: C 288 TYR cc_start: 0.8689 (m-80) cc_final: 0.8442 (m-80) REVERT: C 333 ASN cc_start: 0.8471 (t0) cc_final: 0.8089 (t0) REVERT: D 54 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8484 (tptp) REVERT: D 80 LYS cc_start: 0.8669 (mttt) cc_final: 0.7953 (tttm) REVERT: D 94 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8320 (mt-10) REVERT: D 249 LYS cc_start: 0.8311 (mmtm) cc_final: 0.8011 (mmtm) REVERT: D 285 LYS cc_start: 0.8585 (tttt) cc_final: 0.7977 (ttmm) REVERT: E 160 LYS cc_start: 0.8409 (tptt) cc_final: 0.7952 (ttpt) REVERT: E 236 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.6118 (tmm) REVERT: E 265 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8221 (mttm) REVERT: E 309 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7827 (t0) REVERT: F 64 HIS cc_start: 0.8181 (p90) cc_final: 0.7929 (p90) REVERT: F 149 ARG cc_start: 0.8518 (ptp-170) cc_final: 0.8230 (ptt180) REVERT: F 188 MET cc_start: 0.7579 (mmt) cc_final: 0.6146 (mpp) REVERT: G 1 MET cc_start: 0.7282 (tmm) cc_final: 0.6851 (tpp) REVERT: G 38 GLN cc_start: 0.8523 (pt0) cc_final: 0.8288 (pt0) REVERT: G 64 HIS cc_start: 0.7592 (p-80) cc_final: 0.7286 (p-80) REVERT: G 146 LYS cc_start: 0.7611 (tptp) cc_final: 0.7105 (mmmt) REVERT: G 245 PHE cc_start: 0.7964 (p90) cc_final: 0.7372 (p90) REVERT: G 247 GLN cc_start: 0.7975 (mt0) cc_final: 0.7725 (mt0) REVERT: H 72 LEU cc_start: 0.6070 (mm) cc_final: 0.5651 (mm) outliers start: 72 outliers final: 46 residues processed: 572 average time/residue: 0.1456 time to fit residues: 127.8225 Evaluate side-chains 541 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 492 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 168 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 193 optimal weight: 0.7980 chunk 217 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 317 HIS C 171 GLN D 311 ASN E 74 GLN F 27 ASN ** F 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.170278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.123628 restraints weight = 24509.081| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.01 r_work: 0.2986 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21806 Z= 0.148 Angle : 0.549 10.802 29659 Z= 0.281 Chirality : 0.042 0.177 3451 Planarity : 0.004 0.047 3618 Dihedral : 14.635 125.228 3277 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.18 % Allowed : 17.96 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.16), residues: 2555 helix: 0.68 (0.15), residues: 1202 sheet: -0.60 (0.22), residues: 520 loop : -1.31 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 681 TYR 0.019 0.001 TYR G 211 PHE 0.010 0.001 PHE E 328 TRP 0.007 0.001 TRP A 638 HIS 0.009 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (21806) covalent geometry : angle 0.54915 / 0.28 (29659) hydrogen bonds : bond 0.03838 / 2.53 ( 1105) hydrogen bonds : angle 4.43542 / 3.12 ( 3121) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 509 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8018 (mttt) cc_final: 0.7319 (mtmt) REVERT: A 318 MET cc_start: 0.7799 (mmm) cc_final: 0.7301 (mmm) REVERT: A 399 MET cc_start: 0.7375 (ptp) cc_final: 0.7006 (ptm) REVERT: A 474 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: A 570 ARG cc_start: 0.7764 (mtp85) cc_final: 0.7528 (mtp85) REVERT: A 580 LEU cc_start: 0.9184 (tt) cc_final: 0.8574 (tp) REVERT: A 600 ARG cc_start: 0.7419 (ptp-110) cc_final: 0.7120 (ptp-110) REVERT: A 604 LEU cc_start: 0.8526 (mt) cc_final: 0.8243 (mt) REVERT: A 691 ARG cc_start: 0.7631 (tpt-90) cc_final: 0.7419 (tpt170) REVERT: A 767 LYS cc_start: 0.6080 (mtmm) cc_final: 0.5870 (mtmm) REVERT: B 35 GLN cc_start: 0.7737 (tp40) cc_final: 0.7291 (tp40) REVERT: B 160 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8860 (mm) REVERT: B 182 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7565 (mm-30) REVERT: B 237 LYS cc_start: 0.8919 (ttmt) cc_final: 0.8671 (ttmm) REVERT: C 19 TYR cc_start: 0.9227 (m-80) cc_final: 0.8866 (m-80) REVERT: C 78 MET cc_start: 0.8537 (mpp) cc_final: 0.8062 (mpp) REVERT: C 207 ARG cc_start: 0.8576 (tpt-90) cc_final: 0.8233 (tpt90) REVERT: C 223 ASP cc_start: 0.7205 (m-30) cc_final: 0.6922 (m-30) REVERT: C 333 ASN cc_start: 0.8528 (t0) cc_final: 0.8175 (t0) REVERT: D 51 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8266 (mmmm) REVERT: D 54 LYS cc_start: 0.8661 (mmmt) cc_final: 0.8418 (tptp) REVERT: D 80 LYS cc_start: 0.8685 (mttt) cc_final: 0.8018 (tttm) REVERT: D 88 MET cc_start: 0.8032 (tpt) cc_final: 0.7829 (tmm) REVERT: D 285 LYS cc_start: 0.8595 (tttt) cc_final: 0.7998 (ttmm) REVERT: E 160 LYS cc_start: 0.8267 (tptt) cc_final: 0.7854 (ttpt) REVERT: E 265 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8319 (mttm) REVERT: E 272 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7594 (mmtt) REVERT: F 64 HIS cc_start: 0.8109 (p90) cc_final: 0.7891 (p90) REVERT: F 91 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8516 (mt) REVERT: F 150 ASP cc_start: 0.8331 (m-30) cc_final: 0.8057 (m-30) REVERT: F 188 MET cc_start: 0.7604 (mmt) cc_final: 0.6219 (mpp) REVERT: G 1 MET cc_start: 0.7212 (tmm) cc_final: 0.6848 (tpp) REVERT: G 38 GLN cc_start: 0.8558 (pt0) cc_final: 0.8282 (pt0) REVERT: G 64 HIS cc_start: 0.7678 (p-80) cc_final: 0.7294 (p-80) REVERT: G 146 LYS cc_start: 0.7590 (tptp) cc_final: 0.7139 (mmmt) REVERT: G 245 PHE cc_start: 0.7875 (p90) cc_final: 0.7287 (p90) REVERT: G 247 GLN cc_start: 0.7998 (mt0) cc_final: 0.7727 (mt0) REVERT: H 70 MET cc_start: 0.3774 (OUTLIER) cc_final: 0.3552 (tmm) REVERT: H 72 LEU cc_start: 0.5987 (mm) cc_final: 0.5673 (mm) REVERT: H 181 ILE cc_start: 0.7431 (mt) cc_final: 0.6938 (tp) REVERT: H 204 ASP cc_start: 0.5894 (m-30) cc_final: 0.5145 (m-30) outliers start: 73 outliers final: 45 residues processed: 547 average time/residue: 0.1535 time to fit residues: 128.1669 Evaluate side-chains 537 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 488 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 34 optimal weight: 2.9990 chunk 247 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 21 optimal weight: 0.0770 chunk 223 optimal weight: 0.0970 chunk 3 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 151 HIS F 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.171869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.125018 restraints weight = 24459.680| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.82 r_work: 0.3055 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21806 Z= 0.109 Angle : 0.521 12.067 29659 Z= 0.266 Chirality : 0.040 0.164 3451 Planarity : 0.004 0.048 3618 Dihedral : 14.576 125.404 3274 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.40 % Allowed : 18.53 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.17), residues: 2555 helix: 0.95 (0.15), residues: 1205 sheet: -0.33 (0.22), residues: 525 loop : -1.07 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 681 TYR 0.020 0.001 TYR A 302 PHE 0.010 0.001 PHE H 28 TRP 0.006 0.001 TRP D 295 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (21806) covalent geometry : angle 0.52111 / 0.27 (29659) hydrogen bonds : bond 0.03387 / 2.23 ( 1105) hydrogen bonds : angle 4.32086 / 3.04 ( 3121) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 514 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8072 (mttt) cc_final: 0.7338 (mtmt) REVERT: A 318 MET cc_start: 0.7849 (mmm) cc_final: 0.7352 (mmm) REVERT: A 399 MET cc_start: 0.7363 (ptp) cc_final: 0.6920 (ptm) REVERT: A 474 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: A 600 ARG cc_start: 0.7326 (ptp-110) cc_final: 0.7066 (ptp-110) REVERT: A 604 LEU cc_start: 0.8522 (mt) cc_final: 0.8234 (mt) REVERT: B 160 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8952 (mm) REVERT: B 182 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7701 (mm-30) REVERT: B 237 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8660 (ttmm) REVERT: B 238 LYS cc_start: 0.8759 (ttpt) cc_final: 0.8428 (tttp) REVERT: C 19 TYR cc_start: 0.9257 (m-80) cc_final: 0.8924 (m-80) REVERT: C 78 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8035 (mpp) REVERT: C 207 ARG cc_start: 0.8615 (tpt-90) cc_final: 0.8270 (tpt90) REVERT: C 223 ASP cc_start: 0.7238 (m-30) cc_final: 0.6798 (m-30) REVERT: C 333 ASN cc_start: 0.8629 (t0) cc_final: 0.8292 (t0) REVERT: D 54 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8430 (tptp) REVERT: D 80 LYS cc_start: 0.8719 (mttt) cc_final: 0.8013 (tttm) REVERT: D 96 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7721 (m-40) REVERT: D 208 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8620 (mm-30) REVERT: D 285 LYS cc_start: 0.8560 (tttt) cc_final: 0.7982 (ttmm) REVERT: E 160 LYS cc_start: 0.8249 (tptt) cc_final: 0.7804 (ttpt) REVERT: E 265 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8359 (mttm) REVERT: E 272 LYS cc_start: 0.7814 (mmtt) cc_final: 0.7579 (mmtt) REVERT: F 64 HIS cc_start: 0.8136 (p90) cc_final: 0.7912 (p90) REVERT: F 91 ILE cc_start: 0.8834 (mt) cc_final: 0.8606 (mt) REVERT: F 188 MET cc_start: 0.7643 (mmt) cc_final: 0.6204 (mpp) REVERT: G 1 MET cc_start: 0.7222 (tmm) cc_final: 0.6857 (tpp) REVERT: G 38 GLN cc_start: 0.8599 (pt0) cc_final: 0.8213 (pt0) REVERT: G 64 HIS cc_start: 0.7772 (p-80) cc_final: 0.7378 (p-80) REVERT: G 146 LYS cc_start: 0.7572 (tptp) cc_final: 0.7147 (mmmt) REVERT: G 245 PHE cc_start: 0.8033 (p90) cc_final: 0.7430 (p90) REVERT: G 247 GLN cc_start: 0.8063 (mt0) cc_final: 0.7781 (mt0) REVERT: G 254 PHE cc_start: 0.6229 (m-10) cc_final: 0.5924 (m-80) REVERT: H 72 LEU cc_start: 0.6010 (mm) cc_final: 0.5614 (mm) REVERT: H 161 MET cc_start: 0.5931 (mtp) cc_final: 0.5720 (mtp) REVERT: H 181 ILE cc_start: 0.7410 (mt) cc_final: 0.6916 (tp) REVERT: H 204 ASP cc_start: 0.6019 (m-30) cc_final: 0.5666 (m-30) outliers start: 78 outliers final: 50 residues processed: 560 average time/residue: 0.1459 time to fit residues: 125.7111 Evaluate side-chains 549 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 495 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 165 optimal weight: 0.0020 chunk 251 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 256 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 779 HIS B 26 ASN B 177 GLN C 12 ASN D 340 HIS E 74 GLN F 27 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.164144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.117019 restraints weight = 24384.812| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.85 r_work: 0.2945 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 21806 Z= 0.258 Angle : 0.647 13.197 29659 Z= 0.328 Chirality : 0.045 0.164 3451 Planarity : 0.005 0.046 3618 Dihedral : 14.764 128.481 3274 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.97 % Allowed : 19.92 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.17), residues: 2555 helix: 0.74 (0.15), residues: 1207 sheet: -0.42 (0.22), residues: 531 loop : -0.79 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 206 TYR 0.035 0.002 TYR E 42 PHE 0.016 0.002 PHE F 248 TRP 0.013 0.002 TRP A 638 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.26 (21806) covalent geometry : angle 0.64719 / 0.33 (29659) hydrogen bonds : bond 0.04503 / 2.96 ( 1105) hydrogen bonds : angle 4.53490 / 3.18 ( 3121) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 502 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8167 (mttt) cc_final: 0.7429 (mtmm) REVERT: A 318 MET cc_start: 0.7943 (mmm) cc_final: 0.7472 (mmm) REVERT: A 347 ARG cc_start: 0.7559 (ptm160) cc_final: 0.7024 (ptp-170) REVERT: A 350 MET cc_start: 0.7800 (tpp) cc_final: 0.7367 (tpp) REVERT: A 352 TYR cc_start: 0.8202 (p90) cc_final: 0.7960 (p90) REVERT: A 399 MET cc_start: 0.7449 (ptp) cc_final: 0.7005 (ptm) REVERT: A 474 GLN cc_start: 0.7949 (tt0) cc_final: 0.7188 (tm-30) REVERT: A 580 LEU cc_start: 0.9203 (tp) cc_final: 0.8664 (tp) REVERT: A 600 ARG cc_start: 0.7601 (ptp-110) cc_final: 0.7396 (ptp-110) REVERT: A 679 TYR cc_start: 0.7665 (m-80) cc_final: 0.7226 (m-80) REVERT: B 35 GLN cc_start: 0.8031 (tp40) cc_final: 0.7271 (tp40) REVERT: B 160 ILE cc_start: 0.9349 (mm) cc_final: 0.9065 (mm) REVERT: B 165 LYS cc_start: 0.8832 (mttt) cc_final: 0.8526 (mttm) REVERT: B 181 LEU cc_start: 0.8765 (mt) cc_final: 0.8347 (mm) REVERT: B 182 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7780 (mm-30) REVERT: B 237 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8755 (ttmm) REVERT: C 75 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.7303 (t80) REVERT: C 78 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8522 (mpp) REVERT: C 184 HIS cc_start: 0.7529 (m-70) cc_final: 0.6469 (t-170) REVERT: C 223 ASP cc_start: 0.7552 (m-30) cc_final: 0.7075 (m-30) REVERT: C 225 ASP cc_start: 0.8707 (p0) cc_final: 0.8417 (p0) REVERT: C 333 ASN cc_start: 0.8726 (t0) cc_final: 0.8279 (t0) REVERT: D 54 LYS cc_start: 0.8699 (mmmt) cc_final: 0.8479 (tptp) REVERT: D 80 LYS cc_start: 0.8764 (mttt) cc_final: 0.7985 (tttm) REVERT: D 285 LYS cc_start: 0.8600 (tttt) cc_final: 0.7983 (ttmm) REVERT: E 42 TYR cc_start: 0.9021 (p90) cc_final: 0.8782 (p90) REVERT: E 118 GLN cc_start: 0.6924 (mp10) cc_final: 0.6534 (mm-40) REVERT: E 160 LYS cc_start: 0.8484 (tptt) cc_final: 0.7963 (ttpt) REVERT: E 163 LYS cc_start: 0.8352 (mttt) cc_final: 0.7723 (tptt) REVERT: E 265 LYS cc_start: 0.8644 (mtmt) cc_final: 0.8379 (mttm) REVERT: E 280 ILE cc_start: 0.8616 (mt) cc_final: 0.8360 (tp) REVERT: F 8 GLU cc_start: 0.7491 (pm20) cc_final: 0.7279 (pm20) REVERT: F 79 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8966 (mt) REVERT: F 91 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8630 (mt) REVERT: F 188 MET cc_start: 0.7662 (mmt) cc_final: 0.6251 (mpp) REVERT: F 242 LYS cc_start: 0.8332 (mtmm) cc_final: 0.7882 (mmmm) REVERT: G 1 MET cc_start: 0.7168 (tmm) cc_final: 0.6898 (tpp) REVERT: G 38 GLN cc_start: 0.8628 (pt0) cc_final: 0.8359 (pt0) REVERT: G 64 HIS cc_start: 0.8021 (p-80) cc_final: 0.7576 (p-80) REVERT: G 146 LYS cc_start: 0.7603 (tptp) cc_final: 0.7135 (mmmt) REVERT: G 158 ILE cc_start: 0.7205 (mm) cc_final: 0.6914 (pt) REVERT: G 254 PHE cc_start: 0.6459 (m-80) cc_final: 0.6054 (m-80) REVERT: H 72 LEU cc_start: 0.6018 (mm) cc_final: 0.5571 (mm) REVERT: H 161 MET cc_start: 0.6048 (mtp) cc_final: 0.5700 (mtp) REVERT: H 181 ILE cc_start: 0.7465 (mt) cc_final: 0.6987 (tp) REVERT: H 246 LEU cc_start: 0.2689 (OUTLIER) cc_final: 0.2377 (mt) outliers start: 91 outliers final: 71 residues processed: 555 average time/residue: 0.1437 time to fit residues: 122.5919 Evaluate side-chains 555 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 479 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 256 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 156 optimal weight: 0.0670 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 122 optimal weight: 0.4980 chunk 139 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 231 optimal weight: 8.9990 chunk 241 optimal weight: 30.0000 chunk 180 optimal weight: 5.9990 chunk 230 optimal weight: 40.0000 chunk 64 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 171 GLN E 74 GLN G 58 GLN ** G 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.168332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.121579 restraints weight = 24360.454| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.99 r_work: 0.2985 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21806 Z= 0.118 Angle : 0.544 14.473 29659 Z= 0.277 Chirality : 0.041 0.154 3451 Planarity : 0.004 0.060 3618 Dihedral : 14.618 123.983 3274 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.05 % Allowed : 21.27 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.17), residues: 2555 helix: 1.00 (0.15), residues: 1209 sheet: -0.26 (0.22), residues: 527 loop : -0.71 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 68 TYR 0.017 0.001 TYR E 42 PHE 0.012 0.001 PHE G 6 TRP 0.009 0.001 TRP A 669 HIS 0.006 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (21806) covalent geometry : angle 0.54441 / 0.28 (29659) hydrogen bonds : bond 0.03521 / 2.33 ( 1105) hydrogen bonds : angle 4.38376 / 3.08 ( 3121) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 511 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8105 (mttt) cc_final: 0.7342 (mtmm) REVERT: A 318 MET cc_start: 0.7920 (mmm) cc_final: 0.7457 (mmm) REVERT: A 347 ARG cc_start: 0.7588 (ptm160) cc_final: 0.7064 (ptp-170) REVERT: A 350 MET cc_start: 0.7732 (tpp) cc_final: 0.7289 (tpp) REVERT: A 388 LEU cc_start: 0.8684 (mt) cc_final: 0.8243 (mt) REVERT: A 399 MET cc_start: 0.7376 (ptp) cc_final: 0.6974 (ptm) REVERT: A 474 GLN cc_start: 0.7929 (tt0) cc_final: 0.7262 (tm-30) REVERT: A 580 LEU cc_start: 0.9222 (tp) cc_final: 0.8838 (tp) REVERT: B 35 GLN cc_start: 0.7996 (tp40) cc_final: 0.7280 (tp40) REVERT: B 160 ILE cc_start: 0.9331 (mm) cc_final: 0.9043 (mm) REVERT: B 165 LYS cc_start: 0.8728 (mttt) cc_final: 0.8459 (mttm) REVERT: B 182 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 237 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8734 (ttmm) REVERT: B 238 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8251 (tttp) REVERT: C 19 TYR cc_start: 0.9302 (m-80) cc_final: 0.9056 (m-80) REVERT: C 78 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8234 (mpp) REVERT: C 184 HIS cc_start: 0.7429 (m-70) cc_final: 0.6515 (t-170) REVERT: C 207 ARG cc_start: 0.8677 (tpt-90) cc_final: 0.8408 (tpt90) REVERT: C 221 ASN cc_start: 0.6854 (m-40) cc_final: 0.6535 (m110) REVERT: C 223 ASP cc_start: 0.7482 (m-30) cc_final: 0.7060 (m-30) REVERT: C 256 TRP cc_start: 0.9296 (OUTLIER) cc_final: 0.7730 (t60) REVERT: C 333 ASN cc_start: 0.8754 (t0) cc_final: 0.8364 (t0) REVERT: D 57 ASN cc_start: 0.8825 (p0) cc_final: 0.8493 (p0) REVERT: D 80 LYS cc_start: 0.8716 (mttt) cc_final: 0.8022 (tttm) REVERT: D 96 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7923 (m-40) REVERT: D 285 LYS cc_start: 0.8609 (tttt) cc_final: 0.7990 (ttmm) REVERT: E 42 TYR cc_start: 0.9048 (p90) cc_final: 0.8756 (p90) REVERT: E 118 GLN cc_start: 0.6958 (mp10) cc_final: 0.6545 (mm-40) REVERT: E 160 LYS cc_start: 0.8441 (tptt) cc_final: 0.7930 (ttpt) REVERT: E 163 LYS cc_start: 0.8323 (mttt) cc_final: 0.7658 (tptt) REVERT: E 265 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8460 (mttm) REVERT: E 280 ILE cc_start: 0.8634 (mt) cc_final: 0.8395 (tp) REVERT: F 8 GLU cc_start: 0.7459 (pm20) cc_final: 0.7211 (pm20) REVERT: F 91 ILE cc_start: 0.8834 (mt) cc_final: 0.8616 (mt) REVERT: F 188 MET cc_start: 0.7647 (mmt) cc_final: 0.6242 (mpp) REVERT: F 242 LYS cc_start: 0.8301 (mtmm) cc_final: 0.7880 (mmmm) REVERT: G 1 MET cc_start: 0.7209 (tmm) cc_final: 0.6900 (tpp) REVERT: G 38 GLN cc_start: 0.8588 (pt0) cc_final: 0.8240 (pt0) REVERT: G 64 HIS cc_start: 0.8030 (p-80) cc_final: 0.7649 (p-80) REVERT: G 120 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7157 (m-30) REVERT: G 143 GLU cc_start: 0.7218 (pm20) cc_final: 0.6865 (pm20) REVERT: G 146 LYS cc_start: 0.7596 (tptp) cc_final: 0.7142 (mmmt) REVERT: G 245 PHE cc_start: 0.8099 (p90) cc_final: 0.7422 (p90) REVERT: G 254 PHE cc_start: 0.6375 (m-80) cc_final: 0.6021 (m-80) REVERT: H 250 LEU cc_start: 0.3940 (OUTLIER) cc_final: 0.3545 (mt) outliers start: 70 outliers final: 53 residues processed: 555 average time/residue: 0.1542 time to fit residues: 130.8686 Evaluate side-chains 555 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 497 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 256 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 32 optimal weight: 0.0370 chunk 3 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN E 74 GLN F 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.166986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.119900 restraints weight = 24456.079| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.86 r_work: 0.2983 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21806 Z= 0.152 Angle : 0.569 15.113 29659 Z= 0.287 Chirality : 0.042 0.144 3451 Planarity : 0.004 0.064 3618 Dihedral : 14.600 129.691 3274 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.75 % Allowed : 21.27 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.17), residues: 2555 helix: 1.07 (0.15), residues: 1208 sheet: -0.16 (0.22), residues: 524 loop : -0.66 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 600 TYR 0.014 0.001 TYR A 302 PHE 0.011 0.001 PHE D 290 TRP 0.008 0.001 TRP A 669 HIS 0.005 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (21806) covalent geometry : angle 0.56871 / 0.29 (29659) hydrogen bonds : bond 0.03662 / 2.41 ( 1105) hydrogen bonds : angle 4.37129 / 3.07 ( 3121) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 499 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8055 (mttt) cc_final: 0.7359 (mtmm) REVERT: A 318 MET cc_start: 0.7884 (mmm) cc_final: 0.7436 (mmm) REVERT: A 347 ARG cc_start: 0.7582 (ptm160) cc_final: 0.7061 (ptp-170) REVERT: A 350 MET cc_start: 0.7736 (tpp) cc_final: 0.7279 (tpp) REVERT: A 388 LEU cc_start: 0.8682 (mt) cc_final: 0.8223 (mt) REVERT: A 399 MET cc_start: 0.7390 (ptp) cc_final: 0.7002 (ptm) REVERT: A 474 GLN cc_start: 0.7934 (tt0) cc_final: 0.7213 (tm-30) REVERT: A 580 LEU cc_start: 0.9195 (tp) cc_final: 0.8822 (tp) REVERT: B 35 GLN cc_start: 0.7969 (tp40) cc_final: 0.7250 (tp40) REVERT: B 77 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: B 160 ILE cc_start: 0.9310 (mm) cc_final: 0.9014 (mm) REVERT: B 165 LYS cc_start: 0.8736 (mttt) cc_final: 0.8443 (mttm) REVERT: B 182 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7751 (mm-30) REVERT: B 238 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8211 (tttp) REVERT: C 19 TYR cc_start: 0.9346 (m-80) cc_final: 0.9035 (m-80) REVERT: C 78 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8295 (mpp) REVERT: C 223 ASP cc_start: 0.7617 (m-30) cc_final: 0.7229 (m-30) REVERT: C 256 TRP cc_start: 0.9320 (OUTLIER) cc_final: 0.7766 (t60) REVERT: C 333 ASN cc_start: 0.8770 (t0) cc_final: 0.8358 (t0) REVERT: D 57 ASN cc_start: 0.8855 (p0) cc_final: 0.8487 (p0) REVERT: D 80 LYS cc_start: 0.8664 (mttt) cc_final: 0.7964 (tttm) REVERT: D 88 MET cc_start: 0.8263 (tmm) cc_final: 0.7762 (tmm) REVERT: D 96 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7904 (m-40) REVERT: D 285 LYS cc_start: 0.8525 (tttt) cc_final: 0.7898 (ttmm) REVERT: E 118 GLN cc_start: 0.6959 (mp10) cc_final: 0.6572 (mm-40) REVERT: E 160 LYS cc_start: 0.8453 (tptt) cc_final: 0.7917 (ttpt) REVERT: E 163 LYS cc_start: 0.8351 (mttt) cc_final: 0.7690 (tptt) REVERT: E 256 LYS cc_start: 0.8481 (mmmt) cc_final: 0.7694 (mmtp) REVERT: E 265 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8399 (mttm) REVERT: E 280 ILE cc_start: 0.8654 (mt) cc_final: 0.8333 (tp) REVERT: F 8 GLU cc_start: 0.7480 (pm20) cc_final: 0.7229 (pm20) REVERT: F 91 ILE cc_start: 0.8832 (mt) cc_final: 0.8619 (mt) REVERT: F 188 MET cc_start: 0.7661 (mmt) cc_final: 0.6261 (mpp) REVERT: F 242 LYS cc_start: 0.8323 (mtmm) cc_final: 0.7881 (mmmm) REVERT: G 1 MET cc_start: 0.7229 (tmm) cc_final: 0.6939 (tpp) REVERT: G 38 GLN cc_start: 0.8573 (pt0) cc_final: 0.8261 (pt0) REVERT: G 64 HIS cc_start: 0.8048 (p-80) cc_final: 0.7679 (p-80) REVERT: G 146 LYS cc_start: 0.7596 (tptp) cc_final: 0.7130 (mmmt) REVERT: G 245 PHE cc_start: 0.7930 (p90) cc_final: 0.7318 (p90) REVERT: H 126 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6557 (mm) REVERT: H 181 ILE cc_start: 0.7431 (mt) cc_final: 0.6954 (tp) REVERT: H 250 LEU cc_start: 0.3954 (OUTLIER) cc_final: 0.3574 (mt) outliers start: 86 outliers final: 69 residues processed: 554 average time/residue: 0.1521 time to fit residues: 129.7123 Evaluate side-chains 561 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 486 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 159 GLU Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 256 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 5 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 165 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 171 GLN D 303 GLN E 74 GLN F 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.166819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.119927 restraints weight = 24499.321| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.83 r_work: 0.2978 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21806 Z= 0.147 Angle : 0.571 18.398 29659 Z= 0.286 Chirality : 0.041 0.152 3451 Planarity : 0.004 0.053 3618 Dihedral : 14.546 130.381 3274 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.62 % Allowed : 21.75 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.17), residues: 2555 helix: 1.13 (0.15), residues: 1209 sheet: -0.11 (0.22), residues: 524 loop : -0.61 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 600 TYR 0.026 0.001 TYR E 42 PHE 0.011 0.001 PHE D 290 TRP 0.008 0.001 TRP A 669 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (21806) covalent geometry : angle 0.57073 / 0.29 (29659) hydrogen bonds : bond 0.03617 / 2.38 ( 1105) hydrogen bonds : angle 4.35945 / 3.06 ( 3121) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 494 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8053 (mttt) cc_final: 0.7387 (mtmm) REVERT: A 347 ARG cc_start: 0.7541 (ptm160) cc_final: 0.7097 (ptp-170) REVERT: A 350 MET cc_start: 0.7723 (tpp) cc_final: 0.7268 (tpp) REVERT: A 388 LEU cc_start: 0.8720 (mt) cc_final: 0.8262 (mt) REVERT: A 399 MET cc_start: 0.7446 (ptp) cc_final: 0.7088 (ptm) REVERT: A 474 GLN cc_start: 0.7933 (tt0) cc_final: 0.7197 (tm-30) REVERT: A 580 LEU cc_start: 0.9224 (tp) cc_final: 0.8844 (tp) REVERT: B 35 GLN cc_start: 0.7936 (tp40) cc_final: 0.7312 (tp40) REVERT: B 77 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: B 160 ILE cc_start: 0.9339 (mm) cc_final: 0.9028 (mm) REVERT: B 165 LYS cc_start: 0.8721 (mttt) cc_final: 0.8440 (mttm) REVERT: B 182 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7711 (mm-30) REVERT: B 237 LYS cc_start: 0.9032 (ttmt) cc_final: 0.8790 (ttmm) REVERT: B 238 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8238 (tttp) REVERT: B 297 MET cc_start: 0.8807 (mtp) cc_final: 0.8461 (mtp) REVERT: C 19 TYR cc_start: 0.9307 (m-80) cc_final: 0.8998 (m-80) REVERT: C 68 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.8187 (mtm-85) REVERT: C 78 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8395 (mpp) REVERT: C 207 ARG cc_start: 0.8667 (tpt-90) cc_final: 0.8393 (tpt90) REVERT: C 223 ASP cc_start: 0.7518 (m-30) cc_final: 0.7100 (m-30) REVERT: C 256 TRP cc_start: 0.9286 (OUTLIER) cc_final: 0.7800 (t60) REVERT: C 333 ASN cc_start: 0.8734 (t0) cc_final: 0.8346 (t0) REVERT: D 80 LYS cc_start: 0.8707 (mttt) cc_final: 0.8026 (tttm) REVERT: D 88 MET cc_start: 0.8299 (tmm) cc_final: 0.7809 (tmm) REVERT: D 96 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7918 (m-40) REVERT: D 285 LYS cc_start: 0.8560 (tttt) cc_final: 0.7955 (ttmm) REVERT: E 118 GLN cc_start: 0.6887 (mp10) cc_final: 0.6488 (mm-40) REVERT: E 160 LYS cc_start: 0.8491 (tptt) cc_final: 0.8010 (ttpt) REVERT: E 256 LYS cc_start: 0.8467 (mmmt) cc_final: 0.7679 (mmtp) REVERT: E 265 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8439 (mttm) REVERT: F 8 GLU cc_start: 0.7430 (pm20) cc_final: 0.7175 (pm20) REVERT: F 91 ILE cc_start: 0.8821 (mt) cc_final: 0.8616 (mt) REVERT: F 188 MET cc_start: 0.7718 (mmt) cc_final: 0.6298 (mpp) REVERT: F 242 LYS cc_start: 0.8318 (mtmm) cc_final: 0.7909 (mmmm) REVERT: G 38 GLN cc_start: 0.8588 (pt0) cc_final: 0.8340 (pt0) REVERT: G 64 HIS cc_start: 0.8176 (p-80) cc_final: 0.7816 (p-80) REVERT: G 120 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7135 (m-30) REVERT: G 146 LYS cc_start: 0.7619 (tptp) cc_final: 0.7167 (mmmt) REVERT: G 247 GLN cc_start: 0.8084 (mt0) cc_final: 0.7547 (mt0) REVERT: H 126 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6504 (mm) REVERT: H 181 ILE cc_start: 0.7463 (mt) cc_final: 0.6969 (tp) REVERT: H 250 LEU cc_start: 0.3753 (OUTLIER) cc_final: 0.3397 (mt) outliers start: 83 outliers final: 66 residues processed: 544 average time/residue: 0.1487 time to fit residues: 124.3112 Evaluate side-chains 559 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 486 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 70 MET Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 256 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 137 optimal weight: 1.9990 chunk 63 optimal weight: 0.0060 chunk 99 optimal weight: 0.8980 chunk 256 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 214 optimal weight: 0.0870 chunk 35 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.5374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 171 GLN E 74 GLN F 27 ASN G 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.168869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.122282 restraints weight = 24366.754| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.82 r_work: 0.3015 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21806 Z= 0.109 Angle : 0.550 17.835 29659 Z= 0.276 Chirality : 0.040 0.173 3451 Planarity : 0.004 0.064 3618 Dihedral : 14.426 129.162 3274 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.05 % Allowed : 22.54 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.17), residues: 2555 helix: 1.31 (0.15), residues: 1207 sheet: 0.06 (0.23), residues: 523 loop : -0.56 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 67 TYR 0.029 0.001 TYR A 302 PHE 0.010 0.001 PHE D 290 TRP 0.008 0.001 TRP D 324 HIS 0.003 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (21806) covalent geometry : angle 0.55042 / 0.28 (29659) hydrogen bonds : bond 0.03275 / 2.16 ( 1105) hydrogen bonds : angle 4.30154 / 3.02 ( 3121) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 502 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8041 (mttt) cc_final: 0.7328 (mtmm) REVERT: A 318 MET cc_start: 0.7832 (mmm) cc_final: 0.7624 (mmm) REVERT: A 347 ARG cc_start: 0.7477 (ptm160) cc_final: 0.7076 (ptp-170) REVERT: A 388 LEU cc_start: 0.8701 (mt) cc_final: 0.8252 (mt) REVERT: A 399 MET cc_start: 0.7343 (ptp) cc_final: 0.6966 (ptm) REVERT: A 474 GLN cc_start: 0.7912 (tt0) cc_final: 0.7239 (tm-30) REVERT: A 489 THR cc_start: 0.8759 (m) cc_final: 0.8472 (p) REVERT: A 544 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7449 (mt-10) REVERT: A 580 LEU cc_start: 0.9179 (tp) cc_final: 0.8831 (tp) REVERT: A 594 GLU cc_start: 0.8613 (tp30) cc_final: 0.8210 (tp30) REVERT: A 691 ARG cc_start: 0.7957 (tmt-80) cc_final: 0.7704 (tmt-80) REVERT: B 35 GLN cc_start: 0.7944 (tp40) cc_final: 0.7306 (tp40) REVERT: B 77 GLU cc_start: 0.7943 (tt0) cc_final: 0.7560 (tt0) REVERT: B 160 ILE cc_start: 0.9321 (mm) cc_final: 0.9011 (mm) REVERT: B 182 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7675 (mm-30) REVERT: B 216 HIS cc_start: 0.8002 (m-70) cc_final: 0.7776 (m90) REVERT: B 237 LYS cc_start: 0.9015 (ttmt) cc_final: 0.8792 (ttmm) REVERT: B 238 LYS cc_start: 0.8794 (ttpt) cc_final: 0.8241 (tttp) REVERT: C 19 TYR cc_start: 0.9267 (m-80) cc_final: 0.8996 (m-80) REVERT: C 68 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.8089 (mtm-85) REVERT: C 184 HIS cc_start: 0.7468 (m-70) cc_final: 0.6553 (t-170) REVERT: C 207 ARG cc_start: 0.8578 (tpt-90) cc_final: 0.8300 (tpt90) REVERT: C 223 ASP cc_start: 0.7509 (m-30) cc_final: 0.7124 (m-30) REVERT: C 256 TRP cc_start: 0.9268 (OUTLIER) cc_final: 0.7952 (t60) REVERT: C 333 ASN cc_start: 0.8714 (t0) cc_final: 0.8360 (t0) REVERT: D 51 LYS cc_start: 0.8454 (mmmm) cc_final: 0.8169 (mmmm) REVERT: D 57 ASN cc_start: 0.8922 (p0) cc_final: 0.8634 (p0) REVERT: D 80 LYS cc_start: 0.8678 (mttt) cc_final: 0.8000 (tttm) REVERT: D 88 MET cc_start: 0.8265 (tmm) cc_final: 0.7730 (tmm) REVERT: D 96 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7883 (m-40) REVERT: D 285 LYS cc_start: 0.8525 (tttt) cc_final: 0.7914 (ttmm) REVERT: E 118 GLN cc_start: 0.6917 (mp10) cc_final: 0.6531 (mm-40) REVERT: E 160 LYS cc_start: 0.8426 (tptt) cc_final: 0.7962 (ttpt) REVERT: E 163 LYS cc_start: 0.8364 (mttt) cc_final: 0.7675 (tptt) REVERT: E 256 LYS cc_start: 0.8371 (mmmt) cc_final: 0.7653 (mmtp) REVERT: E 265 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8446 (mttm) REVERT: F 8 GLU cc_start: 0.7398 (pm20) cc_final: 0.7140 (pm20) REVERT: F 91 ILE cc_start: 0.8804 (mt) cc_final: 0.8602 (mt) REVERT: F 188 MET cc_start: 0.7662 (mmt) cc_final: 0.6232 (mpp) REVERT: F 242 LYS cc_start: 0.8298 (mtmm) cc_final: 0.7905 (mmmm) REVERT: G 38 GLN cc_start: 0.8516 (pt0) cc_final: 0.8281 (pt0) REVERT: G 64 HIS cc_start: 0.8030 (p-80) cc_final: 0.7701 (p-80) REVERT: G 120 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7186 (m-30) REVERT: G 146 LYS cc_start: 0.7611 (tptp) cc_final: 0.7154 (mmmt) REVERT: G 245 PHE cc_start: 0.7812 (p90) cc_final: 0.7294 (p90) REVERT: G 247 GLN cc_start: 0.7878 (mt0) cc_final: 0.7475 (mt0) REVERT: H 7 GLU cc_start: 0.7335 (mp0) cc_final: 0.7057 (mp0) REVERT: H 126 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6543 (mm) REVERT: H 181 ILE cc_start: 0.7428 (mt) cc_final: 0.6936 (tp) REVERT: H 250 LEU cc_start: 0.3774 (OUTLIER) cc_final: 0.3426 (mt) outliers start: 70 outliers final: 56 residues processed: 548 average time/residue: 0.1592 time to fit residues: 133.2168 Evaluate side-chains 551 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 490 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 256 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 151 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 235 optimal weight: 40.0000 chunk 202 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 211 optimal weight: 0.2980 chunk 4 optimal weight: 0.0040 chunk 116 optimal weight: 0.0770 chunk 11 optimal weight: 8.9990 overall best weight: 0.4350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 171 GLN E 74 GLN G 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.169643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.122894 restraints weight = 24424.520| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.81 r_work: 0.3027 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 21806 Z= 0.108 Angle : 0.553 17.742 29659 Z= 0.277 Chirality : 0.040 0.152 3451 Planarity : 0.004 0.055 3618 Dihedral : 14.373 128.823 3274 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.88 % Allowed : 23.06 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.17), residues: 2555 helix: 1.35 (0.15), residues: 1215 sheet: 0.14 (0.23), residues: 523 loop : -0.50 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 67 TYR 0.044 0.001 TYR E 42 PHE 0.010 0.001 PHE D 290 TRP 0.007 0.001 TRP D 324 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (21806) covalent geometry : angle 0.55309 / 0.28 (29659) hydrogen bonds : bond 0.03240 / 2.13 ( 1105) hydrogen bonds : angle 4.27497 / 3.00 ( 3121) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 496 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LYS cc_start: 0.8039 (mttt) cc_final: 0.7347 (mtmm) REVERT: A 318 MET cc_start: 0.7838 (mmm) cc_final: 0.7620 (mmm) REVERT: A 347 ARG cc_start: 0.7478 (ptm160) cc_final: 0.7073 (ptp-170) REVERT: A 365 LEU cc_start: 0.8215 (mm) cc_final: 0.8013 (mp) REVERT: A 388 LEU cc_start: 0.8735 (mt) cc_final: 0.8269 (mt) REVERT: A 399 MET cc_start: 0.7310 (ptp) cc_final: 0.6949 (ptm) REVERT: A 474 GLN cc_start: 0.7881 (tt0) cc_final: 0.7161 (tm-30) REVERT: A 489 THR cc_start: 0.8742 (m) cc_final: 0.8494 (p) REVERT: A 521 LEU cc_start: 0.8942 (mp) cc_final: 0.8654 (mp) REVERT: A 580 LEU cc_start: 0.9162 (tp) cc_final: 0.8799 (tp) REVERT: A 691 ARG cc_start: 0.7998 (tmt-80) cc_final: 0.7763 (tmt-80) REVERT: B 35 GLN cc_start: 0.7937 (tp40) cc_final: 0.7342 (tp40) REVERT: B 77 GLU cc_start: 0.7932 (tt0) cc_final: 0.7547 (tt0) REVERT: B 160 ILE cc_start: 0.9309 (mm) cc_final: 0.9002 (mm) REVERT: B 182 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7691 (mm-30) REVERT: B 216 HIS cc_start: 0.7998 (m-70) cc_final: 0.7784 (m90) REVERT: B 237 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8807 (ttmm) REVERT: B 238 LYS cc_start: 0.8810 (ttpt) cc_final: 0.8256 (tttp) REVERT: B 297 MET cc_start: 0.8740 (mtp) cc_final: 0.8408 (mtp) REVERT: C 19 TYR cc_start: 0.9266 (m-80) cc_final: 0.9004 (m-80) REVERT: C 68 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.8092 (mtm-85) REVERT: C 184 HIS cc_start: 0.7468 (m-70) cc_final: 0.6550 (t-170) REVERT: C 207 ARG cc_start: 0.8543 (tpt-90) cc_final: 0.8269 (tpt90) REVERT: C 223 ASP cc_start: 0.7483 (m-30) cc_final: 0.7068 (m-30) REVERT: C 256 TRP cc_start: 0.9268 (OUTLIER) cc_final: 0.7993 (t60) REVERT: C 333 ASN cc_start: 0.8708 (t0) cc_final: 0.8372 (t0) REVERT: D 47 THR cc_start: 0.9261 (m) cc_final: 0.8879 (p) REVERT: D 51 LYS cc_start: 0.8372 (mmmm) cc_final: 0.8083 (mmmm) REVERT: D 57 ASN cc_start: 0.8936 (p0) cc_final: 0.8534 (p0) REVERT: D 80 LYS cc_start: 0.8661 (mttt) cc_final: 0.7999 (tttm) REVERT: D 88 MET cc_start: 0.8246 (tmm) cc_final: 0.7750 (tmm) REVERT: D 96 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7845 (m-40) REVERT: D 285 LYS cc_start: 0.8524 (tttt) cc_final: 0.7910 (ttmm) REVERT: E 118 GLN cc_start: 0.6907 (mp10) cc_final: 0.6530 (mm-40) REVERT: E 160 LYS cc_start: 0.8405 (tptt) cc_final: 0.7949 (ttpt) REVERT: E 236 MET cc_start: 0.6717 (ttm) cc_final: 0.6369 (tmm) REVERT: E 256 LYS cc_start: 0.8389 (mmmt) cc_final: 0.7661 (mmtp) REVERT: E 265 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8428 (mttm) REVERT: F 8 GLU cc_start: 0.7373 (pm20) cc_final: 0.7137 (pm20) REVERT: F 188 MET cc_start: 0.7638 (mmt) cc_final: 0.6225 (mpp) REVERT: F 242 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7898 (mmmm) REVERT: G 38 GLN cc_start: 0.8491 (pt0) cc_final: 0.8283 (pt0) REVERT: G 64 HIS cc_start: 0.7988 (p-80) cc_final: 0.7661 (p-80) REVERT: G 120 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7213 (m-30) REVERT: G 146 LYS cc_start: 0.7629 (tptp) cc_final: 0.7160 (mmmt) REVERT: G 245 PHE cc_start: 0.7843 (p90) cc_final: 0.7628 (p90) REVERT: G 247 GLN cc_start: 0.7934 (mt0) cc_final: 0.7439 (mt0) REVERT: H 7 GLU cc_start: 0.7295 (mp0) cc_final: 0.7019 (mp0) REVERT: H 55 GLU cc_start: 0.7303 (mp0) cc_final: 0.5318 (pm20) REVERT: H 126 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6537 (mm) REVERT: H 181 ILE cc_start: 0.7481 (mt) cc_final: 0.6985 (tp) REVERT: H 250 LEU cc_start: 0.3762 (OUTLIER) cc_final: 0.3413 (mt) outliers start: 66 outliers final: 53 residues processed: 541 average time/residue: 0.1539 time to fit residues: 127.4993 Evaluate side-chains 548 residues out of total 2294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 490 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 199 MET Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 256 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 197 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 211 optimal weight: 0.3980 chunk 212 optimal weight: 2.9990 chunk 239 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 243 optimal weight: 30.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 171 GLN E 74 GLN G 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.169322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.122572 restraints weight = 24573.339| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.83 r_work: 0.3025 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21806 Z= 0.114 Angle : 0.554 16.613 29659 Z= 0.278 Chirality : 0.040 0.144 3451 Planarity : 0.004 0.052 3618 Dihedral : 14.351 128.324 3274 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.79 % Allowed : 23.02 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.17), residues: 2555 helix: 1.39 (0.15), residues: 1215 sheet: 0.14 (0.23), residues: 524 loop : -0.46 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 67 TYR 0.035 0.001 TYR E 42 PHE 0.020 0.001 PHE A 585 TRP 0.006 0.001 TRP A 327 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (21806) covalent geometry : angle 0.55429 / 0.28 (29659) hydrogen bonds : bond 0.03283 / 2.16 ( 1105) hydrogen bonds : angle 4.25682 / 2.99 ( 3121) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5701.82 seconds wall clock time: 98 minutes 20.84 seconds (5900.84 seconds total)